Enable slow CI test runs and fix identity-only energy-estimator workflows

.github/workflows/build-and-test.yaml

@@ -9,6 +9,12 @@ on:
     - '**'
   merge_group:
   workflow_dispatch:
+    inputs:
+      run_slow_tests:
+        description: Run slow tests
+        required: false
+        default: false
+        type: boolean
 
 concurrency:
   group: ${{ github.workflow }}-${{ github.ref }}
@@ -344,7 +350,7 @@ jobs:
     - name: Run Python tests
       env:
         OMP_NUM_THREADS: ${{ matrix.python-test-threads }}
-        QDK_CHEMISTRY_RUN_SLOW_TESTS: 0
+        QDK_CHEMISTRY_RUN_SLOW_TESTS: ${{ inputs.run_slow_tests && '1' || '0' }}
       working-directory: python
       run: |
         set -e

.pipelines/pip-scripts/bootstrap-conda.sh

@@ -62,75 +62,98 @@ case "$(uname -s):$(uname -m)" in
         ;;
 esac
 
-echo "Installing ${ENSURECONDA_PKG} (on $(uname -s):$(uname -m)) and bootstrapping conda..."
-# Use a throwaway venv so we don't fight PEP 668 (Homebrew Python on macOS
-# and apt Python on Ubuntu 24.04 are both externally managed).
-# Clean any stale venv first (idempotent on self-hosted agents / retries).
-rm -rf /tmp/bootstrap-venv
-python3 -m venv /tmp/bootstrap-venv
-# shellcheck disable=SC1091
-. /tmp/bootstrap-venv/bin/activate
-python3 -m pip install --upgrade pip
-python3 -m pip install "${ENSURECONDA_PKG}"
+# All network-sensitive operations (pip install, conda download, env creation)
+# are wrapped in a single retryable function to handle transient failures.
+_BOOTSTRAP_MAX_ATTEMPTS=3
+_BOOTSTRAP_RETRY_DELAY=30
 
-if [ "$USE_MS_ENSURECONDA" = "1" ]; then
-    # ms-ensureconda's --envfile flag dumps CONDA_BASH_HOOK + friends to a
-    # dotenv file we then source to wire up conda for this shell.
-    python3 -m ensureconda --envfile /tmp/ensureconda.env
-    deactivate
-    set -a; . /tmp/ensureconda.env; set +a
-    # shellcheck disable=SC1090
-    . "$CONDA_BASH_HOOK"
-else
-    # Public ensureconda has no --envfile (it's an ms-ensureconda extension);
-    # it just prints the discovered / installed conda binary path on stdout.
-    # Force it to install conda-standalone (default would be micromamba, which
-    # uses a different CLI: `micromamba shell hook --shell bash` instead of
-    # `conda shell.bash hook`, plus mamba-specific `create`/`activate`).
-    CONDA_EXE=$(python3 -m ensureconda --no-mamba --no-micromamba --conda --conda-exe)
-    deactivate
-    export CONDA_EXE
-    # shellcheck disable=SC1090
-    eval "$("$CONDA_EXE" shell.bash hook)"
-fi
+_bootstrap_conda() {
+    echo "Installing ${ENSURECONDA_PKG} (on $(uname -s):$(uname -m)) and bootstrapping conda..."
+    # Use a throwaway venv so we don't fight PEP 668 (Homebrew Python on macOS
+    # and apt Python on Ubuntu 24.04 are both externally managed).
+    # Clean any stale venv first (idempotent on self-hosted agents / retries).
+    rm -rf /tmp/bootstrap-venv
+    python3 -m venv /tmp/bootstrap-venv
+    # shellcheck disable=SC1091
+    . /tmp/bootstrap-venv/bin/activate
+    python3 -m pip install --upgrade pip
+    python3 -m pip install "${ENSURECONDA_PKG}"
 
-echo "Creating conda environment '${CONDA_ENV_NAME}' with Python ${PYTHON_VERSION}..."
-# Explicitly include `pip` — fresh conda envs created with conda-standalone do
-# not include pip by default, which would break `python3 -m pip ...` below.
-#
-# On Linux x86_64 (ms-ensureconda path) we are running under 1ES network
-# isolation (CFSClean): public conda channels (conda.anaconda.org,
-# repo.anaconda.com) are blocked. Force conda to install everything from the
-# Azure Artifacts feed's Conda channel (proxied through the
-# azure-feed://mseng/Anaconda@Published upstream).
-#
-# The feed exposes its upstream conda channels as named subpaths under
-# /Conda/repo/<channel>/ (the feed root /Conda/repo/ itself returns 404 — it
-# is not a channel). We use `main` (the Anaconda defaults channel that hosts
-# python+pip) and `conda-forge` as a fallback for any package that defaults
-# wouldn't carry.
-#
-# Auth: the conda install shipped by ms-ensureconda has a pre-registered
-# azure_artifacts_conda_auth plugin that injects auth on every Azure
-# Artifacts HTTPS request by reading $ARTIFACTS_CONDA_TOKEN. We just need to
-# set that env var (to the pipeline's System.AccessToken). The plugin then
-# handles auth; the channel URL itself must NOT inline the token (the plugin
-# crashes with UnboundLocalError if the var is missing, even when basic-auth
-# creds are present in the URL).
-#
-# Remove any existing conda env with the same name first (idempotent on
-# self-hosted agents and on retries).
-conda env remove -y -n "${CONDA_ENV_NAME}" 2>/dev/null || true
-if [ "$USE_MS_ENSURECONDA" = "1" ]; then
-    : "${SYSTEM_ACCESSTOKEN:?SYSTEM_ACCESSTOKEN must be set when bootstrapping conda from the Azure Artifacts feed}"
-    { set +x; } 2>/dev/null
-    export ARTIFACTS_CONDA_TOKEN="${SYSTEM_ACCESSTOKEN}"
-    set -x
-    CONDA_FEED_ROOT="https://pkgs.dev.azure.com/ms-azurequantum/AzureQuantum/_packaging/quantum-apps-dependencies/Conda/repo"
-    conda create --override-channels \
-                 --channel "${CONDA_FEED_ROOT}/main" \
-                 --channel "${CONDA_FEED_ROOT}/conda-forge" \
-                 --yes --quiet --name "${CONDA_ENV_NAME}" "python=${PYTHON_VERSION}" pip
-else
-    conda create --yes --quiet --name "${CONDA_ENV_NAME}" "python=${PYTHON_VERSION}" pip
-fi
+    if [ "$USE_MS_ENSURECONDA" = "1" ]; then
+        # ms-ensureconda's --envfile flag dumps CONDA_BASH_HOOK + friends to a
+        # dotenv file we then source to wire up conda for this shell.
+        python3 -m ensureconda --envfile /tmp/ensureconda.env
+        deactivate
+        set -a; . /tmp/ensureconda.env; set +a
+        # shellcheck disable=SC1090
+        . "$CONDA_BASH_HOOK"
+    else
+        # Public ensureconda has no --envfile (it's an ms-ensureconda extension);
+        # it just prints the discovered / installed conda binary path on stdout.
+        # Force it to install conda-standalone (default would be micromamba, which
+        # uses a different CLI: `micromamba shell hook --shell bash` instead of
+        # `conda shell.bash hook`, plus mamba-specific `create`/`activate`).
+        CONDA_EXE=$(python3 -m ensureconda --no-mamba --no-micromamba --conda --conda-exe)
+        deactivate
+        export CONDA_EXE
+        # shellcheck disable=SC1090
+        eval "$("$CONDA_EXE" shell.bash hook)"
+    fi
+
+    echo "Creating conda environment '${CONDA_ENV_NAME}' with Python ${PYTHON_VERSION}..."
+    # Explicitly include `pip` — fresh conda envs created with conda-standalone do
+    # not include pip by default, which would break `python3 -m pip ...` below.
+    #
+    # On Linux x86_64 (ms-ensureconda path) we are running under 1ES network
+    # isolation (CFSClean): public conda channels (conda.anaconda.org,
+    # repo.anaconda.com) are blocked. Force conda to install everything from the
+    # Azure Artifacts feed's Conda channel (proxied through the
+    # azure-feed://mseng/Anaconda@Published upstream).
+    #
+    # The feed exposes its upstream conda channels as named subpaths under
+    # /Conda/repo/<channel>/ (the feed root /Conda/repo/ itself returns 404 — it
+    # is not a channel). We use `main` (the Anaconda defaults channel that hosts
+    # python+pip) and `conda-forge` as a fallback for any package that defaults
+    # wouldn't carry.
+    #
+    # Auth: the conda install shipped by ms-ensureconda has a pre-registered
+    # azure_artifacts_conda_auth plugin that injects auth on every Azure
+    # Artifacts HTTPS request by reading $ARTIFACTS_CONDA_TOKEN. We just need to
+    # set that env var (to the pipeline's System.AccessToken). The plugin then
+    # handles auth; the channel URL itself must NOT inline the token (the plugin
+    # crashes with UnboundLocalError if the var is missing, even when basic-auth
+    # creds are present in the URL).
+    #
+    # Remove any existing conda env with the same name first (idempotent on
+    # self-hosted agents and on retries).
+    conda env remove -y -n "${CONDA_ENV_NAME}" 2>/dev/null || true
+    if [ "$USE_MS_ENSURECONDA" = "1" ]; then
+        : "${SYSTEM_ACCESSTOKEN:?SYSTEM_ACCESSTOKEN must be set when bootstrapping conda from the Azure Artifacts feed}"
+        { set +x; } 2>/dev/null
+        export ARTIFACTS_CONDA_TOKEN="${SYSTEM_ACCESSTOKEN}"
+        set -x
+        CONDA_FEED_ROOT="https://pkgs.dev.azure.com/ms-azurequantum/AzureQuantum/_packaging/quantum-apps-dependencies/Conda/repo"
+        conda create --override-channels \
+                     --channel "${CONDA_FEED_ROOT}/main" \
+                     --channel "${CONDA_FEED_ROOT}/conda-forge" \
+                     --yes --quiet --name "${CONDA_ENV_NAME}" "python=${PYTHON_VERSION}" pip
+    else
+        conda create --yes --quiet --name "${CONDA_ENV_NAME}" "python=${PYTHON_VERSION}" pip
+    fi
+}
+
+_bootstrap_attempt=1
+while true; do
+    if _bootstrap_conda; then
+        break
+    fi
+    if [ "$_bootstrap_attempt" -ge "$_BOOTSTRAP_MAX_ATTEMPTS" ]; then
+        echo "ERROR: bootstrap-conda.sh failed after ${_BOOTSTRAP_MAX_ATTEMPTS} attempts." >&2
+        return 1 2>/dev/null || exit 1
+    fi
+    echo "WARNING: bootstrap attempt ${_bootstrap_attempt}/${_BOOTSTRAP_MAX_ATTEMPTS} failed; retrying in ${_BOOTSTRAP_RETRY_DELAY}s..." >&2
+    sleep "$_BOOTSTRAP_RETRY_DELAY"
+    _bootstrap_attempt=$((_bootstrap_attempt + 1))
+done
+unset _bootstrap_attempt _BOOTSTRAP_MAX_ATTEMPTS _BOOTSTRAP_RETRY_DELAY
+unset -f _bootstrap_conda

.pipelines/python-wheels.yaml

@@ -69,6 +69,10 @@ parameters:
   type: string
   default: None
   displayName: PyPI Development Tag (e.g. 'dev1', 'rc1', etc.)
+- name: runSlowTests
+  type: boolean
+  default: true
+  displayName: Run slow tests
 
 variables:
 - group: QdkChemistry
@@ -169,6 +173,7 @@ extends:
                 dockerImage: mcr.microsoft.com/mirror/docker/library/ubuntu:24.04
                 imageTag: linux/amd64
                 pythonVersion: $(pythonVersion)
+                runSlowTests: ${{ parameters.runSlowTests }}
 
           # Build - Linux ARM64
           - ${{ if and(eq(target.arch, 'aarch64'), eq(target.os, 'linux')) }}:
@@ -191,6 +196,7 @@ extends:
                 dockerImage: mcr.microsoft.com/mirror/docker/library/ubuntu:24.04
                 imageTag: linux/arm64/v8
                 pythonVersion: $(pythonVersion)
+                runSlowTests: ${{ parameters.runSlowTests }}
 
           # Build - macOS ARM64
           - ${{ if eq(target.os, 'macOS') }}:
@@ -211,6 +217,7 @@ extends:
                 agentBuildDirectory: $(Agent.BuildDirectory)
                 pythonVersion: $(pythonVersion)
                 macBuild: ON
+                runSlowTests: ${{ parameters.runSlowTests }}
 
           # SBoM Manifest Generator Task requires we transfer ownership of the wheel directory
           # back to the original base image user

.pipelines/templates/build-pip-wheels.yml

@@ -152,3 +152,4 @@ steps:
                                                       ${{ parameters.libflameVersion }} \
                                                       ${{ parameters.macBuild }}
     displayName: Build wheel (macOS native)
+    retryCountOnTaskFailure: 2

.pipelines/templates/test-pip-wheels.yml

@@ -14,6 +14,9 @@ parameters:
 - name: macBuild
   type: string
   default: OFF
+- name: runSlowTests
+  type: boolean
+  default: true
 
 steps:
 - ${{ if and(eq(parameters.macBuild, 'OFF'), eq(parameters.imageTag, 'linux/amd64')) }}:
@@ -24,6 +27,7 @@ steps:
         -e PIP_INDEX_URL \
         -e SYSTEM_ACCESSTOKEN \
         -e QSHARP_PYTHON_TELEMETRY=false \
+        -e QDK_CHEMISTRY_RUN_SLOW_TESTS=${{ parameters.runSlowTests }} \
         -v ${{ parameters.agentBuildDirectory }}:/workspace \
         -w /workspace/qdk-chemistry/python \
         ${{ parameters.dockerImage }} \
@@ -40,6 +44,7 @@ steps:
         --platform ${{ parameters.imageTag }} \
         -e PIP_INDEX_URL \
         -e QSHARP_PYTHON_TELEMETRY=false \
+        -e QDK_CHEMISTRY_RUN_SLOW_TESTS=${{ parameters.runSlowTests }} \
         -v ${{ parameters.agentBuildDirectory }}:/workspace \
         -w /workspace/qdk-chemistry/python \
         ${{ parameters.dockerImage }} \
@@ -51,6 +56,7 @@ steps:
   - script: |
       echo "Running wheel tests (native)..."
       cd ${{ parameters.agentBuildDirectory }}/qdk-chemistry/python
+      export QDK_CHEMISTRY_RUN_SLOW_TESTS=${{ parameters.runSlowTests }}
       bash ../.pipelines/pip-scripts/test-pip-wheels.sh ${{ parameters.pythonVersion }} \
                                                         ${{ parameters.macBuild }}
     displayName: Test wheel (native)

docs/source/_static/examples/python/quickstart.py

@@ -126,9 +126,12 @@
     "circuit_executor",
     AlgorithmRef("circuit_executor", "qdk_full_state_simulator"),
 )
+term_grouper = create("term_grouper", "qubit_wise_commuting")
+grouped_hamiltonian = term_grouper.run(qubit_hamiltonian=qubit_hamiltonian)
+
 energy_results, simulation_data = estimator.run(
     circuit=sparse_isometry_circuit,
-    qubit_hamiltonian=qubit_hamiltonian,
+    qubit_hamiltonian=grouped_hamiltonian,
     total_shots=500000,
 )
 

examples/qpe_stretched_n2.ipynb

@@ -9,13 +9,13 @@
     "\n",
     "This notebook provides an example of `qdk-chemistry` functionality through an end-to-end workflow estimating the ground state energy of a multi-configurational quantum chemistry system.  This is one example of a wide range of functionality in `qdk-chemistry`. Please see <https://github.com/microsoft/qdk-chemistry> for the full documentation.\n",
     "\n",
-    "In addition to [installing `qdk-chemistry`](https://github.com/microsoft/qdk-chemistry/blob/main/INSTALL.md), you will need to install the `jupyter` extra to run this notebook:\n",
+    "In addition to [installing `qdk-chemistry`](https://github.com/microsoft/qdk-chemistry/blob/main/INSTALL.md), you will need to install the `jupyter` and `qiskit-extras` extras to run this notebook:\n",
     "\n",
     "```bash\n",
-    "pip install 'qdk-chemistry[jupyter]'\n",
+    "pip install 'qdk-chemistry[jupyter,qiskit-extras]'\n",
     "```\n",
     "\n",
-    "This installs the additional dependencies required by this notebook (ipykernel, pandas, and pyscf)."
+    "This installs the additional dependencies required by this notebook (ipykernel, pandas, pyscf, qiskit)."
    ]
   },
   {

examples/state_prep_energy.ipynb

@@ -10,13 +10,13 @@
     "This notebook demonstrates an end-to-end multi-configurational quantum chemistry workflow using `qdk-chemistry`.\n",
     "It covers molecule loading and visualization, self-consistent-field (SCF) calculation, active-space selection, multi-configurational wavefunction generation, quantum state-preparation circuit construction, and measurement circuits for energy estimation.\n",
     "\n",
-    "**Prerequisites:** In addition to [installing `qdk-chemistry`](https://github.com/microsoft/qdk-chemistry/blob/main/INSTALL.md), you will need to install the `jupyter` extra to run this notebook:\n",
+    "**Prerequisites:** In addition to [installing `qdk-chemistry`](https://github.com/microsoft/qdk-chemistry/blob/main/INSTALL.md), you will need to install the `jupyter` and `qiskit-extras` extras to run this notebook:\n",
     "\n",
     "```bash\n",
-    "pip install 'qdk-chemistry[jupyter]'\n",
+    "pip install 'qdk-chemistry[jupyter,qiskit-extras]'\n",
     "```\n",
     "\n",
-    "This installs the additional dependencies required by this notebook (ipykernel, pandas, and pyscf).\n",
+    "This installs the additional dependencies required by this notebook (ipykernel, pandas, pyscf, and qiskit).\n",
     "\n",
     "---\n",
     "\n",
@@ -424,9 +424,12 @@
     "    algorithm_name=\"qdk\",\n",
     "    circuit_executor=AlgorithmRef(\"circuit_executor\", \"qdk_sparse_state_simulator\"),\n",
     ")\n",
+    "term_grouper = create(\"term_grouper\", \"qubit_wise_commuting\")\n",
+    "grouped_hamiltonian = term_grouper.run(qubit_hamiltonian=qubit_hamiltonian)\n",
+    "\n",
     "energy_results, simulation_data = estimator.run(\n",
     "    circuit=sparse_isometry_circuit,\n",
-    "    qubit_hamiltonian=qubit_hamiltonian,\n",
+    "    qubit_hamiltonian=grouped_hamiltonian,\n",
     "    total_shots=600000,\n",
     ")\n",
     "\n",